Sodium in PDB 2amf: Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes
Enzymatic activity of Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes
All present enzymatic activity of Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes:
1.2.1.5;
Protein crystallography data
The structure of Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes, PDB code: 2amf
was solved by
B.Nocek,
L.Lezondra,
D.Holzle,
A.Joachimiak,
Midwest Center Forstructural Genomics (Mcsg),
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
50.00 /
2.20
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
171.822,
109.960,
84.158,
90.00,
95.38,
90.00
|
R / Rfree (%)
|
17.3 /
21.5
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes
(pdb code 2amf). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the
Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes, PDB code: 2amf:
Jump to Sodium binding site number:
1;
2;
3;
4;
5;
Sodium binding site 1 out
of 5 in 2amf
Go back to
Sodium Binding Sites List in 2amf
Sodium binding site 1 out
of 5 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na850
b:33.6
occ:1.00
|
O
|
A:GLY89
|
2.2
|
33.6
|
1.0
|
O
|
A:HOH4412
|
2.4
|
36.7
|
1.0
|
O
|
A:HOH4334
|
2.5
|
27.7
|
1.0
|
O
|
A:LEU256
|
2.5
|
37.5
|
1.0
|
O
|
A:ALA253
|
2.6
|
29.7
|
1.0
|
O
|
A:LYS254
|
2.8
|
32.0
|
1.0
|
C
|
A:GLY89
|
3.2
|
33.6
|
1.0
|
C
|
A:LYS254
|
3.3
|
32.6
|
1.0
|
CA
|
A:GLY89
|
3.4
|
33.0
|
1.0
|
C
|
A:LEU256
|
3.5
|
37.5
|
1.0
|
CA
|
A:LYS254
|
3.6
|
32.1
|
1.0
|
C
|
A:ALA253
|
3.6
|
29.6
|
1.0
|
NH1
|
A:ARG94
|
3.9
|
47.3
|
1.0
|
O
|
A:HOH4488
|
3.9
|
49.3
|
1.0
|
N
|
A:LEU256
|
4.0
|
36.2
|
1.0
|
N
|
A:LYS254
|
4.0
|
30.3
|
1.0
|
O
|
A:HOH4343
|
4.1
|
51.5
|
1.0
|
CA
|
A:LEU256
|
4.2
|
36.8
|
1.0
|
N
|
A:SER255
|
4.3
|
33.6
|
1.0
|
N
|
A:ILE90
|
4.4
|
34.1
|
1.0
|
OXT
|
A:LEU256
|
4.4
|
38.2
|
1.0
|
CB
|
A:LEU256
|
4.5
|
36.7
|
1.0
|
C
|
A:SER255
|
4.6
|
35.6
|
1.0
|
O
|
A:HOH4403
|
4.7
|
34.7
|
1.0
|
OD2
|
A:ASP156
|
4.7
|
30.8
|
1.0
|
N
|
A:GLY89
|
4.8
|
32.8
|
1.0
|
CB
|
A:LYS254
|
4.9
|
32.2
|
1.0
|
CA
|
A:SER255
|
4.9
|
34.5
|
1.0
|
CA
|
A:ALA253
|
5.0
|
28.3
|
1.0
|
CA
|
A:ILE90
|
5.0
|
34.1
|
1.0
|
|
Sodium binding site 2 out
of 5 in 2amf
Go back to
Sodium Binding Sites List in 2amf
Sodium binding site 2 out
of 5 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na851
b:35.6
occ:1.00
|
O
|
B:GLY89
|
2.2
|
34.0
|
1.0
|
O
|
B:LEU256
|
2.2
|
36.9
|
1.0
|
O
|
B:HOH4335
|
2.5
|
28.6
|
1.0
|
O
|
B:HOH4394
|
2.5
|
45.0
|
1.0
|
O
|
B:ALA253
|
2.6
|
30.3
|
1.0
|
O
|
B:LYS254
|
2.8
|
34.1
|
1.0
|
C
|
B:GLY89
|
3.2
|
33.8
|
1.0
|
C
|
B:LEU256
|
3.4
|
37.2
|
1.0
|
C
|
B:LYS254
|
3.4
|
33.7
|
1.0
|
CA
|
B:GLY89
|
3.4
|
33.2
|
1.0
|
CA
|
B:LYS254
|
3.6
|
32.9
|
1.0
|
C
|
B:ALA253
|
3.6
|
30.1
|
1.0
|
NH1
|
B:ARG94
|
3.7
|
46.7
|
1.0
|
N
|
B:LYS254
|
4.0
|
30.9
|
1.0
|
O
|
B:HOH4429
|
4.1
|
49.5
|
1.0
|
O
|
B:HOH4362
|
4.1
|
51.2
|
1.0
|
N
|
B:LEU256
|
4.1
|
36.7
|
1.0
|
CA
|
B:LEU256
|
4.2
|
37.0
|
1.0
|
OXT
|
B:LEU256
|
4.2
|
37.7
|
1.0
|
N
|
B:ILE90
|
4.4
|
33.9
|
1.0
|
N
|
B:SER255
|
4.5
|
34.4
|
1.0
|
CB
|
B:LEU256
|
4.5
|
36.7
|
1.0
|
C
|
B:SER255
|
4.6
|
36.2
|
1.0
|
OD2
|
B:ASP156
|
4.6
|
31.6
|
1.0
|
O
|
B:HOH4387
|
4.7
|
36.6
|
1.0
|
N
|
B:GLY89
|
4.9
|
32.9
|
1.0
|
CZ
|
B:ARG94
|
4.9
|
48.4
|
1.0
|
CB
|
B:LYS254
|
4.9
|
33.0
|
1.0
|
CA
|
B:ALA253
|
5.0
|
29.3
|
1.0
|
|
Sodium binding site 3 out
of 5 in 2amf
Go back to
Sodium Binding Sites List in 2amf
Sodium binding site 3 out
of 5 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na852
b:39.0
occ:1.00
|
O
|
C:LEU256
|
2.2
|
37.7
|
1.0
|
O
|
C:GLY89
|
2.4
|
33.9
|
1.0
|
O
|
C:HOH4411
|
2.5
|
45.4
|
1.0
|
O
|
C:ALA253
|
2.5
|
30.1
|
1.0
|
O
|
C:LYS254
|
2.7
|
33.4
|
1.0
|
O
|
C:HOH4332
|
2.8
|
40.3
|
1.0
|
C
|
C:LYS254
|
3.3
|
33.5
|
1.0
|
C
|
C:GLY89
|
3.3
|
34.2
|
1.0
|
C
|
C:LEU256
|
3.4
|
37.4
|
1.0
|
CA
|
C:LYS254
|
3.6
|
32.7
|
1.0
|
CA
|
C:GLY89
|
3.6
|
33.8
|
1.0
|
C
|
C:ALA253
|
3.6
|
30.1
|
1.0
|
N
|
C:LEU256
|
4.0
|
36.4
|
1.0
|
NH1
|
C:ARG94
|
4.0
|
46.5
|
1.0
|
N
|
C:LYS254
|
4.0
|
31.4
|
1.0
|
CA
|
C:LEU256
|
4.2
|
36.8
|
1.0
|
N
|
C:SER255
|
4.2
|
33.9
|
1.0
|
OXT
|
C:LEU256
|
4.3
|
37.9
|
1.0
|
C
|
C:SER255
|
4.4
|
35.8
|
1.0
|
O
|
C:HOH4426
|
4.5
|
43.7
|
1.0
|
O
|
C:HOH4377
|
4.5
|
53.5
|
1.0
|
CB
|
C:LEU256
|
4.5
|
36.5
|
1.0
|
N
|
C:ILE90
|
4.6
|
34.8
|
1.0
|
OD2
|
C:ASP156
|
4.6
|
29.5
|
1.0
|
CA
|
C:SER255
|
4.8
|
35.0
|
1.0
|
CA
|
C:ALA253
|
4.9
|
29.2
|
1.0
|
CB
|
C:LYS254
|
5.0
|
33.0
|
1.0
|
CZ
|
C:ARG94
|
5.0
|
47.8
|
1.0
|
|
Sodium binding site 4 out
of 5 in 2amf
Go back to
Sodium Binding Sites List in 2amf
Sodium binding site 4 out
of 5 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na853
b:33.9
occ:1.00
|
O
|
D:GLY89
|
2.2
|
33.3
|
1.0
|
O
|
D:HOH4486
|
2.3
|
29.9
|
1.0
|
O
|
D:LEU256
|
2.4
|
36.4
|
1.0
|
O
|
D:HOH4485
|
2.5
|
36.8
|
1.0
|
O
|
D:ALA253
|
2.6
|
30.2
|
1.0
|
O
|
D:LYS254
|
2.9
|
33.3
|
1.0
|
C
|
D:GLY89
|
3.2
|
33.5
|
1.0
|
C
|
D:LYS254
|
3.4
|
33.3
|
1.0
|
NH2
|
D:ARG94
|
3.4
|
48.9
|
1.0
|
CA
|
D:GLY89
|
3.5
|
32.8
|
1.0
|
C
|
D:LEU256
|
3.6
|
36.9
|
1.0
|
CA
|
D:LYS254
|
3.6
|
32.8
|
1.0
|
C
|
D:ALA253
|
3.7
|
30.1
|
1.0
|
O
|
D:HOH4452
|
3.8
|
46.1
|
1.0
|
O
|
D:HOH4475
|
4.0
|
55.8
|
1.0
|
N
|
D:LYS254
|
4.1
|
31.3
|
1.0
|
N
|
D:LEU256
|
4.1
|
35.9
|
1.0
|
CA
|
D:LEU256
|
4.3
|
36.6
|
1.0
|
N
|
D:SER255
|
4.4
|
33.9
|
1.0
|
N
|
D:ILE90
|
4.4
|
33.8
|
1.0
|
OXT
|
D:LEU256
|
4.5
|
37.3
|
1.0
|
CZ
|
D:ARG94
|
4.6
|
48.1
|
1.0
|
C
|
D:SER255
|
4.6
|
35.9
|
1.0
|
O
|
D:HOH4374
|
4.7
|
35.9
|
1.0
|
OD2
|
D:ASP156
|
4.7
|
29.5
|
1.0
|
CB
|
D:LEU256
|
4.7
|
36.1
|
1.0
|
O
|
D:HOH4453
|
4.9
|
47.5
|
1.0
|
CB
|
D:LYS254
|
5.0
|
32.9
|
1.0
|
CA
|
D:ILE90
|
5.0
|
34.3
|
1.0
|
N
|
D:GLY89
|
5.0
|
32.8
|
1.0
|
CA
|
D:ALA253
|
5.0
|
29.2
|
1.0
|
|
Sodium binding site 5 out
of 5 in 2amf
Go back to
Sodium Binding Sites List in 2amf
Sodium binding site 5 out
of 5 in the Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 5 of Crystal Structure of 1-Pyrroline-5-Carboxylate Reductase From Human Pathogen Streptococcus Pyogenes within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Na854
b:32.3
occ:1.00
|
O
|
E:LEU256
|
2.2
|
35.5
|
1.0
|
O
|
E:HOH4412
|
2.4
|
29.1
|
1.0
|
O
|
E:GLY89
|
2.4
|
33.3
|
1.0
|
O
|
E:ALA253
|
2.6
|
29.6
|
1.0
|
O
|
E:HOH4419
|
2.6
|
29.6
|
1.0
|
O
|
E:LYS254
|
2.8
|
33.1
|
1.0
|
C
|
E:LYS254
|
3.3
|
33.0
|
1.0
|
C
|
E:GLY89
|
3.3
|
33.0
|
1.0
|
C
|
E:LEU256
|
3.4
|
36.6
|
1.0
|
CA
|
E:GLY89
|
3.5
|
32.7
|
1.0
|
CA
|
E:LYS254
|
3.6
|
32.2
|
1.0
|
NH1
|
E:ARG94
|
3.6
|
45.9
|
1.0
|
C
|
E:ALA253
|
3.7
|
29.7
|
1.0
|
N
|
E:LEU256
|
3.9
|
35.9
|
1.0
|
O
|
E:HOH4422
|
3.9
|
38.0
|
1.0
|
CA
|
E:LEU256
|
4.1
|
36.3
|
1.0
|
N
|
E:LYS254
|
4.1
|
30.5
|
1.0
|
N
|
E:SER255
|
4.2
|
33.4
|
1.0
|
OXT
|
E:LEU256
|
4.3
|
36.7
|
1.0
|
O
|
E:HOH4356
|
4.3
|
41.0
|
1.0
|
C
|
E:SER255
|
4.3
|
35.5
|
1.0
|
O
|
E:HOH4417
|
4.4
|
49.1
|
1.0
|
CB
|
E:LEU256
|
4.5
|
36.0
|
1.0
|
N
|
E:ILE90
|
4.6
|
33.2
|
1.0
|
CA
|
E:SER255
|
4.8
|
34.5
|
1.0
|
OD2
|
E:ASP156
|
4.8
|
30.7
|
1.0
|
CZ
|
E:ARG94
|
4.9
|
47.4
|
1.0
|
O
|
E:SER255
|
4.9
|
36.0
|
1.0
|
CB
|
E:LYS254
|
5.0
|
32.9
|
1.0
|
N
|
E:GLY89
|
5.0
|
32.8
|
1.0
|
CA
|
E:ALA253
|
5.0
|
28.7
|
1.0
|
|
Reference:
B.Nocek,
C.Chang,
H.Li,
L.Lezondra,
D.Holzle,
F.Collart,
A.Joachimiak.
Crystal Structures of Delta(1)-Pyrroline-5-Carboxylate Reductase From Human Pathogens Neisseria Meningitides and Streptococcus Pyogenes J.Mol.Biol. V. 354 91 2005.
ISSN: ISSN 0022-2836
PubMed: 16233902
DOI: 10.1016/J.JMB.2005.08.036
Page generated: Mon Oct 7 01:52:17 2024
|